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| Packages that use de.jstacs.parameters | |
|---|---|
| de.jstacs | This package is the root package for the most and important packages. |
| de.jstacs.algorithms.optimization.termination | |
| de.jstacs.classifier | This package provides the framework for any classifier. |
| de.jstacs.classifier.assessment | This package allows to assess classifiers. |
| de.jstacs.classifier.scoringFunctionBased | Provides the classes for Classifiers that are based on ScoringFunctions. |
| de.jstacs.classifier.scoringFunctionBased.gendismix | Provides an implementation of a classifier that allows to train the parameters of a set of NormalizableScoringFunctions by
a unified generative-discriminative learning principle |
| de.jstacs.classifier.scoringFunctionBased.sampling | Provides the classes for AbstractScoreBasedClassifiers that are based on SamplingScoringFunctions and that sample parameters
using the Metropolis-Hastings algorithm. |
| de.jstacs.data | Provides classes for the representation of data. |
| de.jstacs.data.alphabets | Provides classes for the representation of discrete and continuous alphabets, including a DNAAlphabet for the most common case of DNA-sequences |
| de.jstacs.io | Provides classes for reading data from and writing to a file and storing a number of datatypes, including all primitives, arrays of primitives, and Storables to an XML-representation |
| de.jstacs.models.discrete | |
| de.jstacs.models.discrete.homogeneous.parameters | |
| de.jstacs.models.discrete.inhomogeneous.parameters | |
| de.jstacs.models.hmm | The package provides all interfaces and classes for a hidden Markov model (HMM). |
| de.jstacs.models.hmm.training | The package provides all classes used to determine the training algorithm of a hidden Markov model |
| de.jstacs.parameters | This package provides classes for parameters that establish a general convention for the description of parameters
as defined in the Parameter-interface. |
| de.jstacs.parameters.validation | Provides classes for the validation of Parameter values |
| de.jstacs.results | This package provides classes for results and sets of results. |
| de.jstacs.sampling | This package contains many classes that can be used while a sampling. |
| de.jstacs.scoringFunctions.directedGraphicalModels | Provides ScoringFunctions that are equivalent to directed graphical models. |
| de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures | Provides the facilities to learn the structure of a BayesianNetworkScoringFunction. |
| de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures | Provides the facilities to learn the structure of a BayesianNetworkScoringFunction as
a Bayesian tree using a number of measures to define a rating of structures |
| de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures | Provides the facilities to learn the structure of a BayesianNetworkScoringFunction as
a permuted Markov model using a number of measures to define a rating of structures |
| de.jstacs.utils | This package contains a bundle of useful classes and interfaces like ... |
| de.jstacs.utils.galaxy | |
| Classes in de.jstacs.parameters used by de.jstacs | |
|---|---|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| Classes in de.jstacs.parameters used by de.jstacs.algorithms.optimization.termination | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.classifier | |
|---|---|
| CollectionParameter
Class for a collection parameter, i.e. a parameter that provides some collection of possible values the user can choose from. |
|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| MultiSelectionCollectionParameter
Class for a Parameter that provides a collection of possible values. |
|
| Parameter
Abstract class for a parameter that shall be used as the parameter of some method, constructor, etc. |
|
| ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter. |
|
| Rangeable
Interface for Parameters that potentially can be varied over a
certain interval or a list of values. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| RangeParameter
Class for a parameter wrapper that allows SimpleParameters to be set
to a set of values. |
|
| RangeParameter.Scale
This enum defines possible scales, if RangeParameter.RangeType is
RangeParameter.RangeType.RANGE. |
|
| Classes in de.jstacs.parameters used by de.jstacs.classifier.assessment | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.classifier.scoringFunctionBased | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| Classes in de.jstacs.parameters used by de.jstacs.classifier.scoringFunctionBased.gendismix | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.classifier.scoringFunctionBased.sampling | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.data | |
|---|---|
| ArrayParameterSet
Class for a ParameterSet that consists of a length-Parameter
that defines the length of the array and an array of
ParameterSetContainers of this length. |
|
| ExpandableParameterSet
A class for a ParameterSet that can be expanded by additional
Parameters at runtime. |
|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| Classes in de.jstacs.parameters used by de.jstacs.data.alphabets | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| Classes in de.jstacs.parameters used by de.jstacs.io | |
|---|---|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| Parameter
Abstract class for a parameter that shall be used as the parameter of some method, constructor, etc. |
|
| ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| Classes in de.jstacs.parameters used by de.jstacs.models.discrete | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.models.discrete.homogeneous.parameters | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| Classes in de.jstacs.parameters used by de.jstacs.models.discrete.inhomogeneous.parameters | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.models.hmm | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.models.hmm.training | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.parameters | |
|---|---|
| CollectionParameter
Class for a collection parameter, i.e. a parameter that provides some collection of possible values the user can choose from. |
|
| CollectionParameter.InconsistentCollectionException
This exception is thrown if the CollectionParameter is
inconsistent for some reason. |
|
| ExpandableParameterSet
A class for a ParameterSet that can be expanded by additional
Parameters at runtime. |
|
| FileParameter
Class for a Parameter that represents a local file. |
|
| FileParameter.FileRepresentation
Class that represents a file. |
|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| MultiSelectionCollectionParameter
Class for a Parameter that provides a collection of possible values. |
|
| Parameter
Abstract class for a parameter that shall be used as the parameter of some method, constructor, etc. |
|
| ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| ParameterSet.ParameterList
Class for a List of Parameters that basically
has the same functionality as ArrayList, but additionally takes
care of the references Parameter.parent. |
|
| ParameterSetContainer
Class for a ParameterSetContainer that contains a
ParameterSet as value. |
|
| Rangeable
Interface for Parameters that potentially can be varied over a
certain interval or a list of values. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| RangeParameter
Class for a parameter wrapper that allows SimpleParameters to be set
to a set of values. |
|
| RangeParameter.RangeType
The possible types of defining ranges for a RangeParameter. |
|
| RangeParameter.Scale
This enum defines possible scales, if RangeParameter.RangeType is
RangeParameter.RangeType.RANGE. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| SimpleParameter
Class for a "simple" parameter. |
|
| SimpleParameter.DatatypeNotValidException
Class for an Exception that can be thrown if the provided
int-value that represents a data type is not one of the
values defined in DataType. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| SimpleParameterSet
Class for a ParameterSet that is constructed from an array of Parameters
and thus does nothing in the method SimpleParameterSet.loadParameters(). |
|
| Classes in de.jstacs.parameters used by de.jstacs.parameters.validation | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| Parameter
Abstract class for a parameter that shall be used as the parameter of some method, constructor, etc. |
|
| SimpleParameter
Class for a "simple" parameter. |
|
| Classes in de.jstacs.parameters used by de.jstacs.results | |
|---|---|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.sampling | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.scoringFunctions.directedGraphicalModels | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| Classes in de.jstacs.parameters used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| Classes in de.jstacs.parameters used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| Classes in de.jstacs.parameters used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| Classes in de.jstacs.parameters used by de.jstacs.utils | |
|---|---|
| CollectionParameter
Class for a collection parameter, i.e. a parameter that provides some collection of possible values the user can choose from. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| Classes in de.jstacs.parameters used by de.jstacs.utils.galaxy | |
|---|---|
| ParameterSet
(Container) class for a set of Parameters. |
|
|
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